0.1 By Month

0.2 CCAMLR Units

0.3 Distance

0.4 Time

0.5 Velocity

0.6 Angles

1 Correlated random walk

Process Model

\[ d_{t} \sim T*d_{t-1} + Normal(0,\Sigma)\] \[ x_t = x_{t-1} + d_{t} \]

1.1 Parameters

For each individual:

\[\theta = \text{Mean turning angle}\] \[\gamma = \text{Move persistence} \]

For both behaviors process variance is: \[ \sigma_{latitude} = 0.1\] \[ \sigma_{longitude} = 0.1\]

1.2 Behavioral States

\[ \text{For each individual i}\] \[ Behavior_1 = \text{traveling}\] \[ Behavior_2 = \text{foraging}\]

\[ \alpha_{i,1,1} = \text{Probability of remaining traveling when traveling}\] \[\alpha_{i,2,1} = \text{Probability of switching from Foraging to traveling}\]

\[\begin{matrix} \alpha_{i,1,1} & 1-\alpha_{i,1,1} \\ \alpha_{i,2,1} & 1-\alpha_{i,2,1} \\ \end{matrix}\]

With the probability of switching states:

\[logit(\phi_{traveling}) = \alpha_{Behavior_{t-1}}\]

\[\phi_{foraging} = 1 - \phi_{traveling} \]

1.3 Continious tracks

The transmitter will often go dark for 10 to 12 hours, due to weather, right in the middle of an otherwise good track. The model requires regular intervals to estimate the turning angles and temporal autocorrelation. As a track hits one of these walls, call it the end of a track, and begin a new track once the weather improves. We can remove any micro-tracks that are less than three days. Specify a duration, calculate the number of tracks and the number of removed points. Iteratively.

How did the filter change the extent of tracks?

Look at the observations were defined into tracks.

sink(“Bayesian/Multi_RW.jags”) cat(" model{

#Constants
pi <- 3.141592653589

##argos observation error##
argos_prec[1:2,1:2] <- inverse(argos_sigma*argos_cov[,])

#Constructing the covariance matrix
argos_cov[1,1] <- 1
argos_cov[1,2] <- sqrt(argos_alpha) * rho
argos_cov[2,1] <- sqrt(argos_alpha) * rho
argos_cov[2,2] <- argos_alpha

for(i in 1:ind){
for(g in 1:tracks[i]){

## Priors for first true location
#for lat long
y[i,g,1,1:2] ~ dmnorm(argos[i,g,1,1,1:2],argos_prec)

#First movement - random walk.
y[i,g,2,1:2] ~ dmnorm(y[i,g,1,1:2],iSigma)

###First Behavioral State###
state[i,g,1] ~ dcat(lambda[]) ## assign state for first obs

#Process Model for movement
for(t in 2:(steps[i,g]-1)){

#Behavioral State at time T
phi[i,g,t,1] <- alpha_mu[state[i,g,t-1]] 
phi[i,g,t,2] <- 1-phi[i,g,t,1]
state[i,g,t] ~ dcat(phi[i,g,t,])

#Turning covariate
#Transition Matrix for turning angles
T[i,g,t,1,1] <- cos(theta[state[i,g,t]])
T[i,g,t,1,2] <- (-sin(theta[state[i,g,t]]))
T[i,g,t,2,1] <- sin(theta[state[i,g,t]])
T[i,g,t,2,2] <- cos(theta[state[i,g,t]])

#Correlation in movement change
d[i,g,t,1:2] <- y[i,g,t,] + gamma[state[i,g,t]] * T[i,g,t,,] %*% (y[i,g,t,1:2] - y[i,g,t-1,1:2])

#Gaussian Displacement
y[i,g,t+1,1:2] ~ dmnorm(d[i,g,t,1:2],iSigma)
}

#Final behavior state
phi[i,g,steps[i,g],1] <- alpha_mu[state[i,g,steps[i,g]-1]] 
phi[i,g,steps[i,g],2] <- 1-phi[i,g,steps[i,g],1]
state[i,g,steps[i,g]] ~ dcat(phi[i,g,steps[i,g],])

##  Measurement equation - irregular observations
# loops over regular time intervals (t)    

for(t in 2:steps[i,g]){

# loops over observed locations within interval t
for(u in 1:idx[i,g,t]){ 
zhat[i,g,t,u,1:2] <- (1-j[i,g,t,u]) * y[i,g,t-1,1:2] + j[i,g,t,u] * y[i,g,t,1:2]

#for each lat and long
#argos error
argos[i,g,t,u,1:2] ~ dmnorm(zhat[i,g,t,u,1:2],argos_prec)
}
}
}
}
###Priors###

#Process Variance
iSigma ~ dwish(R,2)
Sigma <- inverse(iSigma)

##Mean Angle
tmp[1] ~ dbeta(20, 20)
tmp[2] ~ dbeta(10, 10)

# prior for theta in 'traveling state'
theta[1] <- (2 * tmp[1] - 1) * pi

# prior for theta in 'foraging state'    
theta[2] <- (tmp[2] * pi * 2)

##Move persistance
# prior for gamma (autocorrelation parameter)
#from jonsen 2016

##Behavioral States

gamma[1] ~ dbeta(4,2)       ## gamma for state 1
dev ~ dbeta(1,1)            ## a random deviate to ensure that gamma[1] > gamma[2]
gamma[2] <- gamma[1] * dev

#gamma[1]<-0.7
#gamma[2]<-0.1

#Intercepts
alpha_mu[1] ~ dbeta(1,1)
alpha_mu[2] ~ dbeta(1,1)

#Probability of behavior switching 
lambda[1] ~ dbeta(1,1)
lambda[2] <- 1 - lambda[1]

##Argos priors##
#longitudinal argos error
argos_sigma ~ dunif(0,10)

#latitidunal argos error
argos_alpha~dunif(0,10)

#correlation in argos error
rho ~ dunif(-1, 1)


}"
,fill=TRUE)

sink()

##     user   system  elapsed 
##    1.266    0.033 3369.234

1.4 Chains

##                           Type     Size    PrettySize  Rows Columns
## mdat                data.frame 16339200 [1] "15.6 Mb" 49859      47
## m                        ggmap 13116336 [1] "12.5 Mb"  1280    1280
## jagM            rjags.parallel  9145008  [1] "8.7 Mb"     6      NA
## b       SpatialPointsDataFrame  5338960  [1] "5.1 Mb"  5081      47
## fccamlr             data.frame  1649608  [1] "1.6 Mb" 41160       7
## sxy                       list  1458976  [1] "1.4 Mb"    22      NA
## data                      list  1428400  [1] "1.4 Mb"     9      NA
## d       SpatialPointsDataFrame  1415872  [1] "1.4 Mb"  5081      47
## mxy                 grouped_df  1384016  [1] "1.3 Mb"  4351      52
## oxy                 data.frame  1331488  [1] "1.3 Mb"  5081      47
##           used (Mb) gc trigger  (Mb) max used  (Mb)
## Ncells 1553728 83.0    2637877 140.9  2637877 140.9
## Vcells 7907446 60.4   33215132 253.5 64872887 495.0

Look at the convergence of phi, just for an example

Overall relationship between phi and state, nice test of convergence.

1.4.1 Compare to priors

1.5 Parameter Summary

##   parameter         par       mean       lower     upper
## 1  alpha_mu alpha_mu[1] 0.91052500  0.79532845 0.9841030
## 2  alpha_mu alpha_mu[2] 0.20877722  0.08929390 0.4298588
## 3     gamma    gamma[1] 0.48503521  0.41429650 0.5954830
## 4     gamma    gamma[2] 0.08868998  0.00644904 0.2580427
## 5     theta    theta[1] 0.03052077 -0.04748132 0.1149233
## 6     theta    theta[2] 2.82255859  1.80110011 3.7972858

2 Behavioral Prediction

Relationship between phi and state

2.1 Spatial Prediction

2.2 By individual

Overlay phi and state

2.3 Compared to CMLRR regions

2.4 Autocorrelation in behavior

2.5 Location of Behavior

3 Overlap with Krill Fishery

4 Time spent in grid cell

4.1 ARS

##                           Type     Size    PrettySize   Rows Columns
## mdat                data.frame 16339200 [1] "15.6 Mb"  49859      47
## temp                     ggmap 13116576 [1] "12.5 Mb"   1280    1280
## pc                      tbl_df  6425376  [1] "6.1 Mb" 121520      10
## b       SpatialPointsDataFrame  5338960  [1] "5.1 Mb"   5081      47
## a                       tbl_df  1667960  [1] "1.6 Mb"  41520       7
## fccamlr             data.frame  1649608  [1] "1.6 Mb"  41160       7
## data                      list  1428400  [1] "1.4 Mb"      9      NA
## d       SpatialPointsDataFrame  1415872  [1] "1.4 Mb"   5081      47
## mxy                 data.frame  1404600  [1] "1.3 Mb"   4124      59
## oxy                 data.frame  1331488  [1] "1.3 Mb"   5081      47
##           used (Mb) gc trigger  (Mb) max used  (Mb)
## Ncells 1616510 86.4    2637877 140.9  2637877 140.9
## Vcells 7627910 58.2   21257684 162.2 64872887 495.0